LAMMPS (27 Nov 2018)
  using 1 OpenMP thread(s) per MPI task
# sample surface deposition script for molecules

units		lj
atom_style      bond
boundary        p p f

lattice		fcc 1.0
Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
region          box block 0 5 0 5 0 10
create_box      3 box bond/types 1 extra/bond/per/atom 1
Created orthogonal box = (0 0 0) to (7.93701 7.93701 15.874)
  1 by 1 by 4 MPI processor grid

region		substrate block INF INF INF INF INF 3
create_atoms	1 region substrate
Created 350 atoms
  Time spent = 0.000594139 secs

pair_style	lj/cut 2.5
pair_coeff	* * 1.0 1.0
pair_coeff	1 2 1.0 1.0 5.0
mass		* 1.0

bond_style	harmonic
bond_coeff      1 5.0 1.0

neigh_modify	delay 0

group		addatoms type 2
0 atoms in group addatoms
region          mobile block 0 5 0 5 2 INF
group		mobile region mobile
150 atoms in group mobile

compute		add addatoms temp
compute_modify	add dynamic/dof yes extra/dof 0

fix		1 addatoms nve
fix		2 mobile langevin 0.1 0.1 0.1 587283
fix		3 mobile nve

molecule        dimer molecule.dimer
Read molecule dimer:
  2 atoms with max type 3
  1 bonds with max type 1
  0 angles with max type 0
  0 dihedrals with max type 0
  0 impropers with max type 0
region          slab block 0 5 0 5 8 9
fix		4 addatoms deposit 100 0 100 12345 region slab near 1.0                 mol dimer vz -1.0 -1.0
fix		5 addatoms wall/reflect zhi EDGE

thermo_style	custom step atoms temp epair etotal press
thermo          100
thermo_modify	temp add lost/bond ignore lost warn
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)

#dump		1 all atom 50 dump.deposit.atom

#dump		2 all image 50 image.*.jpg type type #		axes yes 0.8 0.02 view 80 -30
#dump_modify	2 pad 5

#dump		3 all movie 50 movie.mpg type type #		axes yes 0.8 0.02 view 80 -30
#dump_modify	3 pad 5

run             10000
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 5.3
  ghost atom cutoff = 5.3
  binsize = 2.65, bins = 3 3 6
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 0.441 | 3.16 | 4.226 Mbytes
Step Atoms Temp E_pair TotEng Press 
       0      350            0   -6.9215833   -6.9215833   -1.0052629 
     100      352   0.83994737   -6.8946578   -6.8874992  -0.73775337 
     200      354   0.83994737   -6.8644786   -6.8502422  -0.69623155 
     300      356   0.84169616   -6.8219435    -6.800657  -0.69554978 
     400      358   0.84705847   -6.7754627   -6.7470538  -0.67243811 
     500      360   0.87562973   -6.7314753   -6.6949361   -0.6950742 
     600      362   0.89546097    -6.710162   -6.6652463  -0.65981803 
     700      364   0.86924248   -6.6786002   -6.6276742  -0.66815906 
     800      366   0.93005193   -6.6524743   -6.5893578  -0.67112658 
     900      368    1.0019234   -6.6197846   -6.5442728  -0.63787501 
    1000      370    1.0088277   -6.5761382   -6.4929294  -0.68476387 
    1100      372   0.95920389   -6.5674754   -6.4791094   -0.6514881 
    1200      374    1.0580798   -6.5939034   -6.4854936  -0.64868897 
    1300      376   0.86424162   -6.5983754   -6.5057565  -0.63699331 
    1400      378   0.67483283   -6.5902961   -6.5114402  -0.65492911 
    1500      380   0.75360589   -6.5780719   -6.4817845  -0.68120797 
    1600      382   0.72620352    -6.569806   -6.4764019  -0.66989877 
    1700      384   0.70645024   -6.5716163   -6.4726668   -0.6613115 
    1800      386   0.69881235   -6.5763765   -6.4705405  -0.63092971 
    1900      388   0.55849097   -6.5759885   -6.4828798  -0.66382981 
    2000      390   0.61872265   -6.5695935   -6.4699984  -0.71796632 
    2100      392    0.5081592   -6.5617458   -6.4722443  -0.63479779 
    2200      394   0.48384274    -6.549079   -6.4615149  -0.66946296 
    2300      396   0.58288701   -6.5480033   -6.4412303  -0.71651424 
    2400      398   0.64008255   -6.5601944    -6.435487  -0.69102232 
    2500      400   0.69425764   -6.5828171   -6.4479527  -0.69066043 
    2600      402   0.64360746   -6.6331402   -6.4757801  -0.69090309 
    2700      404   0.49461099   -6.6579388   -6.5307976  -0.64409671 
    2800      406   0.55547146   -6.6714068   -6.5241964  -0.68541724 
    2900      408   0.50073205    -6.686261   -6.5339011  -0.62669192 
    3000      410   0.53038544   -6.6912316   -6.5383759  -0.66969696 
    3100      412   0.50129241   -6.7018519   -6.5548588  -0.68883024 
    3200      414   0.38030632   -6.6977772    -6.566269  -0.71750777 
    3300      416   0.46068514    -6.727184   -6.5662475  -0.68188023 
    3400      418   0.33822772   -6.7360772   -6.6016113  -0.72454552 
    3500      420   0.36453111    -6.724924   -6.5850647  -0.64608093 
    3600      422   0.36002968   -6.7121585   -6.5780413  -0.72223399 
    3700      424   0.36475294   -6.7260042   -6.5866143  -0.67031145 
    3800      426   0.36718557   -6.7217602   -6.5750235  -0.72937729 
    3900      428   0.37814959   -6.7263989   -6.5726951  -0.71591892 
    4000      430   0.40806996   -6.7375374   -6.5678266  -0.72678943 
    4100      432   0.38045271   -6.7361841    -6.568644  -0.73821367 
    4200      434   0.33066806   -6.7299457     -6.57638  -0.73722947 
    4300      436   0.41794011   -6.7644169    -6.579351  -0.73641289 
    4400      438   0.37024397   -6.7629482   -6.5884866  -0.71240322 
    4500      440   0.40320567   -6.7752853   -6.5850469  -0.77279245 
    4600      442   0.35772381   -6.7835099   -6.6013018  -0.73636644 
    4700      444    0.3651311   -6.7990539   -6.6175275  -0.66854139 
    4800      446   0.35091135    -6.802215   -6.6224615  -0.76162889 
    4900      448   0.36081012   -6.7989512   -6.6125569  -0.76016221 
    5000      450   0.31623339   -6.8039093   -6.6262913  -0.69115281 
    5100      452   0.31543867   -6.7941532   -6.6159299  -0.72205584 
    5200      454   0.36158004   -6.8038417   -6.5978895  -0.76776475 
    5300      456   0.32434144    -6.793123   -6.6082355  -0.72624243 
    5400      458   0.32124677    -6.793797   -6.6010261  -0.67741044 
    5500      460   0.32879658   -6.8125027   -6.6145418  -0.77045881 
    5600      462   0.33544185   -6.8282158   -6.6181936  -0.82298638 
    5700      464   0.31929648   -6.8312019    -6.617542  -0.77506457 
    5800      466   0.38513813   -6.8569307   -6.6094667  -0.72432147 
    5900      468   0.36275508   -6.8784065   -6.6183826  -0.71794686 
    6000      470   0.36550412   -6.8913174   -6.6280912  -0.73323549 
    6100      472   0.31989948   -6.8850192    -6.653122    -0.770755 
    6200      474   0.31533478   -6.8764261   -6.6470078  -0.81602846 
    6300      476   0.33764472   -6.9058038   -6.6574918  -0.70233823 
    6400      478   0.33629492   -6.9384728   -6.6676899    -0.750356 
    6500      480     0.329134   -6.9539905   -6.6660118  -0.76780643 
    6600      482   0.35893902   -6.9727388   -6.6687914  -0.79588633 
    6700      484   0.35256839    -6.980576   -6.6800042  -0.67119736 
    6800      486    0.3498406   -6.9854977   -6.6867156  -0.78135658 
    6900      488   0.31757914   -6.9609817   -6.6859771  -0.78048643 
    7000      490   0.40129918   -6.9903536   -6.6713072  -0.75727925 
    7100      492   0.33833658   -7.0145206   -6.6977622   -0.7587661 
    7200      494   0.35160231   -7.0237931   -6.7095634  -0.67933941 
    7300      496   0.28084778    -7.024433   -6.7195845  -0.82825025 
    7400      498   0.32213221   -7.0527945   -6.7230557  -0.84919299 
    7500      500   0.40905237   -7.1021905   -6.7203497  -0.93185466 
    7600      502    0.3609358   -7.1596615   -6.7690359  -0.64194099 
    7700      504   0.29253629   -7.1428432    -6.796613   -0.6976599 
    7800      506   0.31731365    -7.176045   -6.8068169  -0.87636485 
    7900      508    0.2905957   -7.1788367   -6.8119013  -0.75756081 
    8000      510   0.28404368   -7.1870361    -6.824287  -0.79842667 
    8100      512   0.34219804    -7.222691   -6.8386818  -0.75369138 
    8200      514   0.32055193   -7.2353127   -6.8551345  -0.78172901 
    8300      516   0.30120879   -7.2446887   -6.8672024  -0.83621194 
    8400      518   0.30883515   -7.2596909   -6.8762796  -0.71183282 
    8500      520   0.26204254   -7.2431895   -6.8834311  -0.83712537 
    8600      522   0.29103293   -7.2694658   -6.8867581  -0.82744948 
    8700      524   0.26753583   -7.2593959    -6.889244  -0.78004892 
    8800      526   0.26521096   -7.2599673   -6.8902608  -0.79408301 
    8900      528   0.28003646   -7.2530274   -6.8808417   -0.8606495 
    9000      530   0.26313192   -7.2628164   -6.8855381   -0.7707451 
    9100      532    0.2646514   -7.2830171    -6.893178  -0.76585646 
    9200      534   0.27846656   -7.2721664   -6.8861564  -0.89816607 
    9300      536   0.30560594   -7.2964254   -6.8845198  -0.72034116 
    9400      538   0.29262217   -7.3023252   -6.8913192  -0.62961985 
    9500      540   0.29718418   -7.3048523   -6.8949946  -0.87394403 
    9600      542   0.34146099    -7.349026   -6.9092212  -0.76789895 
    9700      544   0.28703519   -7.3161372   -6.9121067  -0.84885733 
    9800      546   0.28129876   -7.3140275   -6.9098746  -0.82726219 
    9900      548   0.28891495   -7.3235633   -6.9092268  -0.88128702 
   10000      550   0.29861445   -7.3507915   -6.9161229  -0.73192335 
Loop time of 6.59998 on 4 procs for 10000 steps with 550 atoms

Performance: 654547.468 tau/day, 1515.156 timesteps/s
95.1% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.0020502  | 1.124      | 3.2865     | 126.5 | 17.03
Bond    | 0.0019848  | 0.0045845  | 0.011024   |   5.5 |  0.07
Neigh   | 0.0055914  | 0.79469    | 2.5826     | 118.4 | 12.04
Comm    | 0.541      | 3.3411     | 6.0178     | 116.5 | 50.62
Output  | 0.0026808  | 0.018505   | 0.055692   |  15.9 |  0.28
Modify  | 0.017398   | 0.054306   | 0.10289    |  15.9 |  0.82
Other   |            | 1.263      |            |       | 19.13

Nlocal:    137.5 ave 299 max 2 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost:    1866.25 ave 2673 max 377 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs:    9891 ave 24535 max 0 min
Histogram: 2 0 0 0 0 0 1 0 0 1

Total # of neighbors = 39564
Ave neighs/atom = 71.9345
Ave special neighs/atom = 0.363636
Neighbor list builds = 884
Dangerous builds = 0
Total wall time: 0:00:06
